I would like to change the sequence of a particular GenBank file (NC_000913.3) and update its coinciding positions in the CDS and gene entries.
At position 2,173,363, I would like to delete 2 bp. This should decrease the CDS and gene entry for gatC by 2.
At position 3,560,455, I would like to insert a 'G'. This should increase the CDS and gene entry for glpR by 1.
At position 4,296,380, I would like to insert a "CG". This would increase the intergenic region gltT and yjcO by 2.
How would someone accomplish these three different cases using BioPython? The method of doing so isn't clear after reviewing the docs and BioPython cookbook.
The net effect would be changes in co-ordinates that would have to be accounted for annotation of all genes between 2,173,363 and end of the genome. I am not sure if you are going to find a ready made solution for this.
That was my understanding also. I was hoping that there was a built-in function or easy workflow to accomplish this with BioPython. Once I code up the solution, I'll post it here.